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CA3146077A1 - Systemes et procedes pour la preparation d'echantillons, le sequencage d'echantillons, la correction de biais de donnees de sequencage et le controle de qualite - Google Patents

Systemes et procedes pour la preparation d'echantillons, le sequencage d'echantillons, la correction de biais de donnees de sequencage et le controle de qualite

Info

Publication number
CA3146077A1
CA3146077A1 CA3146077A CA3146077A CA3146077A1 CA 3146077 A1 CA3146077 A1 CA 3146077A1 CA 3146077 A CA3146077 A CA 3146077A CA 3146077 A CA3146077 A CA 3146077A CA 3146077 A1 CA3146077 A1 CA 3146077A1
Authority
CA
Canada
Prior art keywords
rna
data
expression data
gene
sequence
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
CA3146077A
Other languages
English (en)
Inventor
Ekaterina Nuzhdina
Alexander BAGAEV
Maksim Chelushkin
Yaroslav Lozinsky
Natalia Miheecheva
Alexander Zaitsev
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
BostonGene Corp
Original Assignee
BostonGene Corp
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by BostonGene Corp filed Critical BostonGene Corp
Publication of CA3146077A1 publication Critical patent/CA3146077A1/fr
Pending legal-status Critical Current

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G16B35/10—Design of libraries
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/30—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indices; for individual health risk assessment
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel sequencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/165—Mathematical modelling, e.g. logarithm, ratio

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Medical Informatics (AREA)
  • Analytical Chemistry (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • Library & Information Science (AREA)
  • Public Health (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Pathology (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Epidemiology (AREA)
  • Primary Health Care (AREA)
  • Biomedical Technology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)

Abstract

L'invention concerne divers procédés de collecte et de traitement d'échantillons de tumeur et/ou de tissu sain pour extraire de l'acide nucléique et effectuer un séquençage d'acide nucléique. L'invention concerne également divers procédés de traitement de données de séquençage d'acide nucléique destinés à éliminer le biais des données de séquençage d'acide nucléique. L'invention concerne en outre divers procédés d'évaluation de la qualité d'informations de séquence d'acide nucléique. L'identité et/ou l'intégrité de données de séquence d'acide nucléique sont évaluées avant l'utilisation des informations de séquence pour une analyse ultérieure (par exemple à des fins diagnostiques, pronostiques ou cliniques). Les procédés permettent à un sujet, un médecin ou un utilisateur de caractériser ou classer divers types de cancer avec précision, et de déterminer ainsi une thérapie ou une combinaison de thérapies qui peuvent être efficaces pour traiter un cancer chez un sujet en fonction de la caractérisation précise.
CA3146077A 2019-07-03 2020-07-03 Systemes et procedes pour la preparation d'echantillons, le sequencage d'echantillons, la correction de biais de donnees de sequencage et le controle de qualite Pending CA3146077A1 (fr)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201962870622P 2019-07-03 2019-07-03
US62/870,622 2019-07-03
US202062991570P 2020-03-18 2020-03-18
US62/991,570 2020-03-18
PCT/IB2020/000928 WO2021028726A2 (fr) 2019-07-03 2020-07-03 Systèmes et procédés pour la préparation d'échantillons, le séquençage d'échantillons, la correction de biais de données de séquençage et le contrôle de qualité

Publications (1)

Publication Number Publication Date
CA3146077A1 true CA3146077A1 (fr) 2021-02-18

Family

ID=71948730

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3146077A Pending CA3146077A1 (fr) 2019-07-03 2020-07-03 Systemes et procedes pour la preparation d'echantillons, le sequencage d'echantillons, la correction de biais de donnees de sequencage et le controle de qualite

Country Status (7)

Country Link
US (3) US12205675B2 (fr)
EP (1) EP3994696A2 (fr)
JP (1) JP2022538499A (fr)
AU (1) AU2020327680A1 (fr)
CA (1) CA3146077A1 (fr)
IL (1) IL289254A (fr)
WO (1) WO2021028726A2 (fr)

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US11094397B2 (en) * 2017-05-12 2021-08-17 Noblis, Inc. Secure communication of sensitive genomic information using probabilistic data structures
CA3146077A1 (fr) 2019-07-03 2021-02-18 Bostongene Corporation Systemes et procedes pour la preparation d'echantillons, le sequencage d'echantillons, la correction de biais de donnees de sequencage et le controle de qualite
US20240076744A1 (en) * 2021-01-21 2024-03-07 Tempus Labs, Inc. METHODS AND SYSTEMS FOR mRNA BOUNDARY ANALYSIS IN NEXT GENERATION SEQUENCING
AU2022275923A1 (en) 2021-05-18 2023-11-23 Bostongene Corporation Techniques for single sample expression projection to an expression cohort sequenced with another protocol
WO2023081117A1 (fr) * 2021-11-02 2023-05-11 The Regents Of The University Of California Ciblage d'immunothérapie
CN114093420B (zh) * 2022-01-11 2022-05-27 山东建筑大学 一种基于XGBoost的DNA重组位点预测方法
WO2023168049A2 (fr) * 2022-03-04 2023-09-07 Bostongene Corporation Signatures d'expression de gène de cytokine
WO2024026275A1 (fr) * 2022-07-29 2024-02-01 Foundation Medicine, Inc. Méthodes et systèmes d'identification de perte d'hétérozygotie des hla-i
WO2024159068A1 (fr) * 2023-01-26 2024-08-02 Twist Bioscience Corporation Contrôle de qualité pour stockage de données d'adn
CN118389712B (zh) * 2024-06-28 2024-09-17 南京农业大学 一种与鸡开产体重性状相关的ncapg-lcorl基因座分子标记及其应用

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Also Published As

Publication number Publication date
AU2020327680A1 (en) 2022-01-20
EP3994696A2 (fr) 2022-05-11
WO2021028726A2 (fr) 2021-02-18
US20210005283A1 (en) 2021-01-07
US20220119881A1 (en) 2022-04-21
US20210005284A1 (en) 2021-01-07
JP2022538499A (ja) 2022-09-02
US12205675B2 (en) 2025-01-21
WO2021028726A3 (fr) 2021-04-29
IL289254A (en) 2022-02-01

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